Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009403.1 Hibiscus syriacus cultivar Beakdansim tig00113332_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 40356
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:7042 original size:14 final size:15
Alignment explanation
Indices: 7018--7048 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
7008 AAAAACAAAC
7018 TAAATTAACATAAAA
1 TAAATTAACATAAAA
7033 TAAA-TAACATAAAA
1 TAAATTAACATAAAA
7047 TA
1 TA
7049 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATTAACATAAAA
Found at i:16452 original size:14 final size:15
Alignment explanation
Indices: 16428--16458 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
16418 AAAAACAAAC
16428 TAAATTAACATAAAA
1 TAAATTAACATAAAA
16443 TAAA-TAACATAAAA
1 TAAATTAACATAAAA
16457 TA
1 TA
16459 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATTAACATAAAA
Found at i:17265 original size:31 final size:31
Alignment explanation
Indices: 17227--17382 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
17217 CCCGAAGGAC
* * *
17227 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
17258 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
17289 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
17320 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
17351 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
17382 C
1 C
17383 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:18110 original size:21 final size:21
Alignment explanation
Indices: 18080--18124 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18070 ATTCTGTCGT
* *
18080 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
18101 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
18122 TTG
1 TTG
18125 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:21158 original size:31 final size:31
Alignment explanation
Indices: 21120--21275 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
21110 CCCGAAGGAC
* * *
21120 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
21151 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
21182 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
21213 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
21244 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
21275 C
1 C
21276 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:22001 original size:21 final size:21
Alignment explanation
Indices: 21971--22015 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21961 ATTCTGTCGT
* *
21971 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
21992 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
22013 TTG
1 TTG
22016 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:24177 original size:18 final size:18
Alignment explanation
Indices: 24150--24184 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24140 TCATATTATA
*
24150 AATTAGTTGATATTAATC
1 AATTAATTGATATTAATC
*
24168 AATTAATTGATCTTAAT
1 AATTAATTGATATTAAT
24185 TAAAAAAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (18 bp):
AATTAATTGATATTAATC
Found at i:32093 original size:14 final size:15
Alignment explanation
Indices: 32069--32099 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
32059 AAAAACAAAC
32069 TAAATTAACATAAAA
1 TAAATTAACATAAAA
32084 TAAA-TAACATAAAA
1 TAAATTAACATAAAA
32098 TA
1 TA
32100 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATTAACATAAAA
Done.